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Preface
System Protection
Assistance
Overview of the 454 Sequencing System Software
Data Acquisition, Data Processing and Data Analysis
Data Processing Options
GS Junior System
Data Output and Folder Structure
Data Acquisition (GS Sequencer and GS Junior Sequencer) Results: the Run Folder
Data Processing (GS Run Processor) Results: the Data Processing Folder
Data Analysis Applications Results
Data Files and Formats
Directory Naming Conventions
Format Requirements for Input FASTA and FASTQ Files
FASTA File Format
FASTQ File Format
Standard File Formats
Composite wells file format
Parameters and Viewable Metrics Files: 454 Parser Format (.parse, .txt)
Image Files (.pif and .png)
Well-Level Signal Data Files (.wells)
Exportable Metrics Files (.csv)
DNA Sequence (FASTA; .fna) and Base Quality Score (.qual) Files
454 Sequencing System “Universal” Accession Numbers
Standard Flowgram Files (.sff)